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peak picking

R Rabl, A Horvath, C Breitschaedel, S Flunkert, H Roemer, B Hutter-Paier
BACKGROUND: Evaluation of motor deficits in rodents is mostly restricted to limb motor tests that are often high stressors for the animals. NEW METHOD: To test rodents for orofacial motor impairments in a stress-free environment, we established the pasta gnawing test by measuring the biting noise of mice that eat a piece of spaghetti. Two parameters were evaluated, the biting speed and the biting peaks per biting episode. To evaluate the power of this test compared to commonly used limb motor and muscle strength tests, three mouse models of Parkinson's disease, amyotrophic lateral sclerosis and Niemann pick disease were tested in the pasta gnawing test, RotaRod and wire suspension test...
October 13, 2016: Journal of Neuroscience Methods
Carsten Jaeger, Friederike Hoffmann, Clemens A Schmitt, Jan Lisec
Gas chromatography using atmospheric pressure chemical ionization coupled to mass spectrometry (GC/APCI-MS) is an emerging metabolomics platform, providing much-enhanced capabilities for structural mass spectrometry as compared to traditional electron ionization (EI)-based techniques. To exploit the potential of GC/APCI-MS for more comprehensive metabolite annotation, a major bottleneck in metabolomics, we here present the novel R-based tool InterpretMSSpectrum assisting in the common task of annotating and evaluating in-source mass spectra as obtained from typical full-scan experiments...
October 4, 2016: Analytical Chemistry
Xavier Domingo-Almenara, Jesus Brezmes, Maria Vinaixa, Sara Samino, Noelia Ramirez, Marta Ramon-Krauel, Carles Lerin, Marta Díaz, Lourdes Ibáñez, Xavier Correig, Alexandre Perera-Lluna, Oscar Yanes
Gas chromatography coupled to mass spectrometry (GC/MS) has been a long-standing approach used for identifying small molecules due to the highly reproducible ionization process of electron impact ionization (EI). However, the use of GC-EI MS in untargeted metabolomics produces large and complex data sets characterized by coeluting compounds and extensive fragmentation of molecular ions caused by the hard electron ionization. In order to identify and extract quantitative information on metabolites across multiple biological samples, integrated computational workflows for data processing are needed...
October 4, 2016: Analytical Chemistry
Ronan Cariou, Elsa Omer, Alexis Léon, Gaud Dervilly-Pinel, Bruno Le Bizec
In the present work, we addressed the question of global seeking/screening organohalogenated compounds in a large panel of complex biological matrices, with a particular focus on unknown chemicals that may be considered as potential emerging hazards. A fishing strategy was developed based on untargeted profiling among full scan acquisition datasets provided by high resolution mass spectrometry. Since large datasets arise from such profiling, filtering useful information stands as a central question. In this way, we took advantage of the exact mass differences between Cl and Br isotopes...
September 14, 2016: Analytica Chimica Acta
Susan Elliott, Norman Buroker, Jason J Cournoyer, Anna M Potier, Joseph D Trometer, Carole Elbin, Mack J Schermer, Jaana Kantola, Aaron Boyce, Frantisek Turecek, Michael H Gelb, C Ronald Scott
In this data article we provide a detailed standard operating procedure for performing a tandem mass spectrometry, multiplex assay of 6 lysosomal enzymes for newborn screening of the lysosomal storage diseases Mucopolysaccharidosis-I, Pompe, Fabry, Niemann-Pick-A/B, Gaucher, and Krabbe, (Elliott, et al., 2016) [1]. We also provide the mass spectrometry peak areas for the product and internal standard ions typically observed with a dried blood spot punch from a random newborn, and we provide the daily variation of the daily mean activities for all 6 enzymes...
September 2016: Data in Brief
Chandan L Barhate, M Farooq Wahab, D J Tognarelli, Terry A Berger, Daniel W Armstrong
It is widely accepted that column technology is ahead of existing chromatographic instruments. The chromatographic output may not reflect the true picture of the peak profile inside the column. The instrumental optimization parameters become far more important when peaks elute in a few seconds. In this work, the low viscosity advantage of the supercritical/subcritical CO2 is coupled with the high efficiency of narrow particle size distribution silica. Using short efficient columns and high flow rates (up to 19 mL/min), separations on the order of a few seconds are demonstrated...
September 6, 2016: Analytical Chemistry
Hannes L Röst, Yansheng Liu, Giuseppe D'Agostino, Matteo Zanella, Pedro Navarro, George Rosenberger, Ben C Collins, Ludovic Gillet, Giuseppe Testa, Lars Malmström, Ruedi Aebersold
Next-generation mass spectrometric (MS) techniques such as SWATH-MS have substantially increased the throughput and reproducibility of proteomic analysis, but ensuring consistent quantification of thousands of peptide analytes across multiple liquid chromatography-tandem MS (LC-MS/MS) runs remains a challenging and laborious manual process. To produce highly consistent and quantitatively accurate proteomics data matrices in an automated fashion, we developed TRIC (, a software tool that utilizes fragment-ion data to perform cross-run alignment, consistent peak-picking and quantification for high-throughput targeted proteomics...
September 2016: Nature Methods
Jia Xu, Steven R Van Doren
Evidence is presented that binding isotherms, simple or biphasic, can be extracted directly from noninterpreted, complex 2D NMR spectra using principal component analysis (PCA) to reveal the largest trend(s) across the series. This approach renders peak picking unnecessary for tracking population changes. In 1:1 binding, the first principal component captures the binding isotherm from NMR-detected titrations in fast, slow, and even intermediate and mixed exchange regimes, as illustrated for phospholigand associations with proteins...
August 16, 2016: Analytical Chemistry
Valerie B Duffy, Shristi Rawal, Jeeha Park, Mark H Brand, Mastaneh Sharafi, Bradley W Bolling
Interest in nutrient-rich berry juices is growing, but their high polyphenol levels render them sensorily unappealing. Fifty adults, who were assessed for sensory phenotype and dietary behaviors, provided sensory and palatability ratings of juices from 'Viking' aronia berries for each of seven harvest weeks. By peak harvest, juice preference increased two-fold, averaging neither like/dislike. This hedonic shift was associated with: increases in juice sugars paralleling increases in perceived sweetness (maximum = weak); reductions in percent acidity paralleling reductions in sourness (minimum = moderate), astringency (minimum = to just above weak) and bitterness (minimum = just below weak)...
July 22, 2016: Appetite
Elsa Gorre, Kevin G Owens
In this work an attenuated total reflection Fourier transform infrared (FT-IR) absorption based method is used to measure the solubility of two matrix-assisted laser desorption-ionization (MALDI) matrices in a few pure solvents and mixtures of acetonitrile and water using low microliter amounts of solution. Results from a method that averages the values obtained from multiple calibration curves created by manual peak picking are compared to those predicted using a partial least squares (PLS) chemometrics approach...
July 19, 2016: Applied Spectroscopy
K Dafopoulos, C I Messini, G Anifandis, P Georgoulias, D Sourlas, I E Messinis
The aim of the present study was to investigate changes of blood ghrelin, adiponectin and resistin levels in IVF/ICSI-ET cycles. Twenty women were stimulated with recombinant FSH in a GnRH agonist short protocol for IVF/ICSI. Blood samples were taken on cycle day 2 before the commencement of injections, on cycle day 6 and on the days of HCG injection, oocyte pick up (OPU), embryo transfer (ET) as well as 7 and 12 days post-ET. Serum E2 levels increased during the stimulation, peaking on the HCG day and declined thereafter (p<0...
July 15, 2016: Physiological Research
R Weiss, A Bitton, M Ben Shimon, S Elhaik Goldman, L Nahary, I Cooper, I Benhar, C G Pick, J Chapman
OBJECTIVES: Antiphospholipid syndrome (APS) is associated with neurological manifestations and one of the novel autoantigens associated with this disease is Annexin A2 (ANXA2). In this work we have examined the effect of high levels of autoantibodies to ANXA2 on the brain in a mouse model. METHODS: Recombinant ANXA2 emulsified in adjuvant was used to immunize mice while mice immunized with adjuvant only served as controls. At peak antibody levels the animal underwent behavioral and cognitive tests and their brains were examined for ANXA2 immunoglobulin G (IgG) and expression of ANXA2 and the closely linked protein p11...
September 2016: Journal of Autoimmunity
Kaiwen Luo, Fang Feng
In this study, a novel untargeted metabolomics-driven strategy based on LC-MS was used to rapidly screen and identify the absorbed components and metabolites of Zhi-Zi-Hou-Po decoction (ZZHPD) in rat plasma. The plasma sample was obtained from orbital venous of rats after oral administration and pretreated by protein precipitation before analysis. All sample data from total ion chromatograms (TICs) of LC-TOF/MS were aligned and peak picked by XCMS and MetAlign combined to extract three-dimensional datasets (peak code, t R -m/z pairs and ion intensity)...
August 2016: Analytical and Bioanalytical Chemistry
Xue Zuo, Hao Hong, Xin-yu Zang, Feng Xu, Ming-ying Shang, Xuan Wang, Shao-qing Cai
This study is to establish the characteristic HPLC chromatogram of phenols in Ephedrae Herba, from which to pick out the marker peaks, followed by the analysis of the regularity of their distribution and content in the herbaceous stems of Ephedra sinica, E. intermedia and E. equisetina. The HPLC-DAD method for the characteristic chromatogram as well as quantitative analysis was established. The separation was carried out on a YMC-Pack ODS-A column (4.6 mm x 250 mm, 5 µm), eluted with the mobile phases as 0...
December 2015: Zhongguo Zhong Yao za Zhi, Zhongguo Zhongyao Zazhi, China Journal of Chinese Materia Medica
Yang Wang, Fang Liu, Peng Li, Chengwei He, Ruibing Wang, Huanxing Su, Jian-Bo Wan
Pseudotargeted metabolomics is a novel strategy integrating the advantages of both untargeted and targeted methods. The conventional pseudotargeted metabolomics required two MS instruments, i.e., ultra-high performance liquid chromatography/quadrupole-time- of-flight mass spectrometry (UHPLC/Q-TOF MS) and UHPLC/triple quadrupole mass spectrometry (UHPLC/QQQ-MS), which makes method transformation inevitable. Furthermore, the picking of ion pairs from thousands of candidates and the swapping of the data between two instruments are the most labor-intensive steps, which greatly limit its application in metabolomic analysis...
July 13, 2016: Analytica Chimica Acta
Massimiliano Sgroi, Paolo Roccaro, Gregory V Korshin, Valentina Greco, Sebastiano Sciuto, Tarun Anumol, Shane A Snyder, Federico G A Vagliasindi
This study investigated the applicability of different techniques for fluorescence excitation/emission matrices data interpretations, including peak-picking method, fluorescence regional integration and PARAFAC modelling, to act as surrogates in predicting emerging trace organic compounds (ETOrCs) removal during conventional wastewater treatments that usually comprise primary and secondary treatments. Results showed that fluorescence indexes developed using alternative methodologies but indicative of a same dissolved organic matter component resulted in similar predictions of the removal of the target compounds...
May 11, 2016: Journal of Hazardous Materials
Xiaokun Hu, Yingyi Luo, Kejun Huang, Yubing Li, Yanwen Xu, Canquan Zhou, Qingyun Mai
The aim of this study was to investigate 2 quantification criteria to evaluate the developmental condition of follicles cohort and clarify their impacts upon the determining of human chorionic gonadotropin trigger timing and the reproductive outcome: the proportion of mature follicles in growing follicles cohort on the day of human chorionic gonadotropin trigger and the peak estradiol level per oocyte on the day of human chorionic gonadotropin administration.Of the patients who underwent in vitro fertilization/ intracytoplasmic sperm injection-embryo transfer from 2011 to 2013, 492 controlled ovarian hyperstimulation cycles using gonadotropin-releasing hormone antagonists reaching the ovum pick-up and fresh embryo-transfer stage were included...
May 2016: Medicine (Baltimore)
Reuben Thomas, Sean Thomas, Alisha K Holloway, Katherine S Pollard
Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is an important tool for studying gene regulatory proteins, such as transcription factors and histones. Peak calling is one of the first steps in the analysis of these data. Peak calling consists of two sub-problems: identifying candidate peaks and testing candidate peaks for statistical significance. We surveyed 30 methods and identified 12 features of the two sub-problems that distinguish methods from each other. We picked six methods GEM, MACS2, MUSIC, BCP, Threshold-based method (TM) and ZINBA] that span this feature space and used a combination of 300 simulated ChIP-seq data sets, 3 real data sets and mathematical analyses to identify features of methods that allow some to perform better than the others...
May 11, 2016: Briefings in Bioinformatics
Shabnam Ajami, Ahmad Mina, Seyed Amin Nabavizadeh
OBJECTIVES: To evaluate the effect of moments and the combination of forces and moments on the mechanical properties of a bracket type miniscrew, resembling engagement of a rectangular wire by three-dimensional (3D) finite element study. MATERIALS AND METHODS: By solid work software (Dassaunlt systems solid works, concord, Mass), a 3D miniscrew model of 6, 8, 10 mm lengths was designed and inserted in the osseous block, consisted of the cortical, and cancellous bones...
April 2016: Journal of Orthodontic Science
Riccardo Di Guida, Jasper Engel, J William Allwood, Ralf J M Weber, Martin R Jones, Ulf Sommer, Mark R Viant, Warwick B Dunn
INTRODUCTION: The generic metabolomics data processing workflow is constructed with a serial set of processes including peak picking, quality assurance, normalisation, missing value imputation, transformation and scaling. The combination of these processes should present the experimental data in an appropriate structure so to identify the biological changes in a valid and robust manner. OBJECTIVES: Currently, different researchers apply different data processing methods and no assessment of the permutations applied to UHPLC-MS datasets has been published...
2016: Metabolomics: Official Journal of the Metabolomic Society
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